# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 23:59:01 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: nonanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCCCCCC(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 AZ1  AZ1  'nonanedioic acid         '  ligand  27  13  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_AZ1
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 AZ1  C1   C  C      0   0.409   0.1135   0.0520   5.1446
 AZ1  C2   C  CH2    0  -0.580  -0.6566   0.0570   3.8125
 AZ1  C3   C  CH2    0  -0.402   0.1889   0.0119   2.5501
 AZ1  C4   C  CH2    0  -0.408  -0.6481   0.0288   1.2761
 AZ1  C5   C  CH2    0  -0.408   0.1899   0.0040   0.0037
 AZ1  C6   C  CH2    0  -0.408  -0.6442   0.0165  -1.2714
 AZ1  C7   C  CH2    0  -0.402   0.1969   0.0138  -2.5428
 AZ1  C8   C  CH2    0  -0.579  -0.6456   0.0177  -3.8080
 AZ1  C9   C  C      0   0.409   0.1286   0.0424  -5.1375
 AZ1  O1   O  OC    -1  -0.635  -0.5695   0.2459   6.1736
 AZ1  O2   O  O      0  -0.610   1.3428  -0.1542   5.1077
 AZ1  O3   O  O      0  -0.611   1.3566   0.2552  -5.0939
 AZ1  O4   O  OC    -1  -0.635  -0.5503  -0.1390  -6.1714
 AZ1  H21  H  HCH2   0   0.211  -1.3059   0.9398   3.7910
 AZ1  H22  H  HCH2   0   0.218  -1.3456  -0.7972   3.8199
 AZ1  H31  H  HCH2   0   0.200   0.8176  -0.8835   2.5560
 AZ1  H32  H  HCH2   0   0.199   0.8788   0.8616   2.5365
 AZ1  H41  H  HCH2   0   0.200  -1.2865   0.9202   1.2695
 AZ1  H42  H  HCH2   0   0.201  -1.3314  -0.8286   1.2767
 AZ1  H51  H  HCH2   0   0.202   0.8314  -0.8849   0.0087
 AZ1  H52  H  HCH2   0   0.202   0.8687   0.8646   0.0009
 AZ1  H61  H  HCH2   0   0.200  -1.2960   0.8983  -1.2682
 AZ1  H62  H  HCH2   0   0.201  -1.3145  -0.8510  -1.2730
 AZ1  H71  H  HCH2   0   0.198   0.8528  -0.8630  -2.5367
 AZ1  H72  H  HCH2   0   0.200   0.8603   0.8833  -2.5374
 AZ1  H81  H  HCH2   0   0.218  -1.3144   0.8881  -3.7950
 AZ1  H82  H  HCH2   0   0.211  -1.3150  -0.8500  -3.8101

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 AZ1  C1  C2   single  1.539  0.020  1.539
 AZ1  C1  O1   deloc   1.250  0.020  1.250
 AZ1  C1  O2   deloc   1.247  0.020  1.247
 AZ1  C2  C3   single  1.520  0.020  1.520
 AZ1  C2  H21  single  0.970  0.020  1.090
 AZ1  C2  H22  single  0.970  0.020  1.090
 AZ1  C3  C4   single  1.524  0.020  1.524
 AZ1  C3  H31  single  0.970  0.020  1.090
 AZ1  C3  H32  single  0.970  0.020  1.090
 AZ1  C4  C5   single  1.524  0.020  1.524
 AZ1  C4  H41  single  0.970  0.020  1.090
 AZ1  C4  H42  single  0.970  0.020  1.090
 AZ1  C5  C6   single  1.524  0.020  1.524
 AZ1  C5  H51  single  0.970  0.020  1.090
 AZ1  C5  H52  single  0.970  0.020  1.090
 AZ1  C6  C7   single  1.524  0.020  1.524
 AZ1  C6  H61  single  0.970  0.020  1.090
 AZ1  C6  H62  single  0.970  0.020  1.090
 AZ1  C7  C8   single  1.520  0.020  1.520
 AZ1  C7  H71  single  0.970  0.020  1.090
 AZ1  C7  H72  single  0.970  0.020  1.090
 AZ1  C8  C9   single  1.539  0.020  1.539
 AZ1  C8  H81  single  0.970  0.020  1.090
 AZ1  C8  H82  single  0.970  0.020  1.090
 AZ1  C9  O3   deloc   1.247  0.020  1.247
 AZ1  C9  O4   deloc   1.250  0.020  1.250

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 AZ1  O2   C1  O1   126.06  3.000
 AZ1  O2   C1  C2   117.92  3.000
 AZ1  O1   C1  C2   116.02  3.000
 AZ1  H22  C2  H21  104.78  3.000
 AZ1  H22  C2  C3   109.37  3.000
 AZ1  H21  C2  C3   109.70  3.000
 AZ1  H22  C2  C1   107.81  3.000
 AZ1  H21  C2  C1   108.42  3.000
 AZ1  C3   C2  C1   116.14  3.000
 AZ1  H32  C3  H31  105.85  3.000
 AZ1  H32  C3  C4   109.09  3.000
 AZ1  H31  C3  C4   109.22  3.000
 AZ1  H32  C3  C2   109.75  3.000
 AZ1  H31  C3  C2   109.84  3.000
 AZ1  C4   C3  C2   112.85  3.000
 AZ1  H42  C4  H41  105.83  3.000
 AZ1  H42  C4  C5   109.30  3.000
 AZ1  H41  C4  C5   109.18  3.000
 AZ1  H42  C4  C3   109.45  3.000
 AZ1  H41  C4  C3   109.50  3.000
 AZ1  C5   C4  C3   113.31  3.000
 AZ1  H52  C5  H51  105.92  3.000
 AZ1  H52  C5  C6   109.29  3.000
 AZ1  H51  C5  C6   109.32  3.000
 AZ1  H52  C5  C4   109.26  3.000
 AZ1  H51  C5  C4   109.35  3.000
 AZ1  C6   C5  C4   113.43  3.000
 AZ1  H62  C6  H61  105.84  3.000
 AZ1  H62  C6  C7   109.55  3.000
 AZ1  H61  C6  C7   109.38  3.000
 AZ1  H62  C6  C5   109.24  3.000
 AZ1  H61  C6  C5   109.24  3.000
 AZ1  C7   C6  C5   113.32  3.000
 AZ1  H72  C7  H71  105.85  3.000
 AZ1  H72  C7  C8   109.77  3.000
 AZ1  H71  C7  C8   109.80  3.000
 AZ1  H72  C7  C6   109.22  3.000
 AZ1  H71  C7  C6   109.11  3.000
 AZ1  C8   C7  C6   112.85  3.000
 AZ1  H82  C8  H81  104.82  3.000
 AZ1  H82  C8  C9   108.56  3.000
 AZ1  H81  C8  C9   107.70  3.000
 AZ1  H82  C8  C7   109.76  3.000
 AZ1  H81  C8  C7   109.26  3.000
 AZ1  C9   C8  C7   116.12  3.000
 AZ1  O4   C9  O3   126.05  3.000
 AZ1  O4   C9  C8   116.04  3.000
 AZ1  O3   C9  C8   117.90  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 AZ1  Var_01  C4  C3  C2  C1  -179.63  30.0  3
 AZ1  Var_02  C5  C4  C3  C2   179.18  30.0  3
 AZ1  Var_03  O1  C1  C2  C3   171.95  30.0  2
 AZ1  Var_04  C6  C5  C4  C3   179.82  30.0  3
 AZ1  Var_05  C7  C6  C5  C4   179.09  30.0  3
 AZ1  Var_06  C8  C7  C6  C5   179.64  30.0  3
 AZ1  Var_07  C9  C8  C7  C6   178.87  30.0  3
 AZ1  Var_08  O3  C9  C8  C7   -10.35  30.0  3

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 AZ1  plan-1  C1  0.020
 AZ1  plan-1  C2  0.020
 AZ1  plan-1  O1  0.020
 AZ1  plan-1  O2  0.020
 AZ1  plan-2  C8  0.020
 AZ1  plan-2  C9  0.020
 AZ1  plan-2  O3  0.020
 AZ1  plan-2  O4  0.020

